Abstract
Dimethylations of histone H3 lysine 9 and lysine 27 are important epigenetic marks associated with transcription repression. Here, we identified KIAA1718 (KDM7A) as a novel histone demethylase specific for these two repressing marks. Using mouse embryonic stem cells, we demonstrated that KIAA1718 expression increased at the early phase of neural differentiation. Knockdown of the gene blocked neural differentiation and the effect was rescued by the wild-type human gene, and not by a catalytically inactive mutant. In addition, overexpression of KIAA1718 accelerated neural differentiation. We provide the evidence that the pro-neural differentiation effect of KDM7A is mediated through direct transcriptional activation of FGF4, a signal molecule implicated in neural differentiation. Thus, our study identified a dual-specificity histone demethylase that regulates neural differentiation through FGF4.
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10 July 2025
A Correction to this paper has been published: https://doi.org/10.1038/s41422-025-01143-2
References
Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ . Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 1997; 389:251–260.
Zhang Y, Reinberg D . Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails. Genes Dev 2001; 15:2343–2360.
Bhaumik SR, Smith E, Shilatifard A . Covalent modifications of histones during development and disease pathogenesis. Nat Struct Mol Biol 2007; 14:1008–1016.
Strahl BD, Allis CD . The language of covalent histone modifications. Nature 2000; 403:41–45.
Peters AH, Kubicek S, Mechtler K, et al. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol Cell 2003; 12:1577–1589.
Rice JC, Briggs SD, Ueberheide B, et al. Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol Cell 2003; 12:1591–1598.
Tachibana M, Sugimoto K, Fukushima T, Shinkai Y . Set domain-containing protein, G9a, is a novel lysine-preferring mammalian histone methyltransferase with hyperactivity and specific selectivity to lysines 9 and 27 of histone H3. J Biol Chem 2001; 276:25309–25317.
Tachibana M, Sugimoto K, Nozaki M, et al. G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis. Genes Dev 2002; 16:1779–1791.
Schultz DC, Ayyanathan K, Negorev D, Maul GG, Rauscher FJ, 3rd. SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Genes Dev 2002; 16:919–932.
Tachibana M, Ueda J, Fukuda M, et al. Histone methyltransferases G9a and GLP form heteromeric complexes and are both crucial for methylation of euchromatin at H3-K9. Genes Dev 2005; 19:815–826.
Wang H, An W, Cao R, et al. mAM facilitates conversion by ESET of dimethyl to trimethyl lysine 9 of histone H3 to cause transcriptional repression. Mol Cell 2003; 12:475–487.
Yang L, Xia L, Wu DY, et al. Molecular cloning of ESET, a novel histone H3-specific methyltransferase that interacts with ERG transcription factor. Oncogene 2002; 21:148–152.
Dodge JE, Kang YK, Beppu H, Lei H, Li E . Histone H3-K9 methyltransferase ESET is essential for early development. Mol Cell Biol 2004; 24:2478–2486.
Barski A, Cuddapah S, Cui K, et al. High-resolution profiling of histone methylations in the human genome. Cell 2007; 129:823–837.
Cao R, Wang L, Wang H, et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 2002; 298:1039–1043.
Kuzmichev A, Nishioka K, Erdjument-Bromage H, Tempst P, Reinberg D . Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev 2002; 16:2893–2905.
Faust C, Lawson KA, Schork NJ, Thiel B, Magnuson T . The Polycomb-group gene eed is required for normal morphogenetic movements during gastrulation in the mouse embryo. Development 1998; 125:4495–4506.
O'Carroll D, Erhardt S, Pagani M, et al. The polycomb-group gene Ezh2 is required for early mouse development. Mol Cell Biol 2001; 21:4330–4336.
Pasini D, Bracken AP, Jensen MR, Lazzerini Denchi E, Helin K . Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity. EMBO J 2004; 23:4061–4071.
Shi Y, Lan F, Matson C, et al. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 2004; 119:941–953.
Tsukada Y, Fang J, Erdjument-Bromage H, et al. Histone demethylation by a family of JmjC domain-containing proteins. Nature 2006; 439:811–816.
Klose RJ, Kallin EM, Zhang Y . JmjC-domain-containing proteins and histone demethylation. Nat Rev Genet 2006; 7:715–727.
Shi Y, Whetstine JR . Dynamic regulation of histone lysine methylation by demethylases. Mol Cell 2007; 25:1–14.
Xiang Y, Zhu Z, Han G, et al. JARID1B is a histone H3 lysine 4 demethylase up-regulated in prostate cancer. Proc Natl Acad Sci USA 2007; 104:19226–19231.
Lee MG, Villa R, Trojer P, et al. Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination. Science 2007; 318:447–450.
Lee MG, Norman J, Shilatifard A, Shiekhattar R . Physical and functional association of a trimethyl H3K4 demethylase and Ring6a/MBLR, a polycomb-like protein. Cell 2007; 128:877–887.
Xiang Y, Zhu Z, Han G, et al. JMJD3 is a histone H3K27 demethylase. Cell Res 2007; 17:850–857.
Lan F, Bayliss PE, Rinn JL, et al. A histone H3 lysine 27 demethylase regulates animal posterior development. Nature 2007; 449:689–694.
Christensen J, Agger K, Cloos PA, et al. RBP2 belongs to a family of demethylases, specific for tri- and dimethylated lysine 4 on histone 3. Cell 2007; 128:1063–1076.
Cloos PA, Christensen J, Agger K, et al. The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3. Nature 2006; 442:307–311.
Iwase S, Lan F, Bayliss P, et al. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell 2007; 128:1077–1088.
Klose RJ, Yamane K, Bae Y, et al. The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36. Nature 2006; 442:312–316.
Klose RJ, Yan Q, Tothova Z, et al. The retinoblastoma binding protein RBP2 is an H3K4 demethylase. Cell 2007; 128:889–900.
Whetstine JR, Nottke A, Lan F, et al. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 2006; 125:467–481.
Yamane K, Tateishi K, Klose RJ, et al. PLU-1 is an H3K4 demethylase involved in transcriptional repression and breast cancer cell proliferation. Mol Cell 2007; 25:801–812.
Yamane K, Toumazou C, Tsukada Y, et al. JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. Cell 2006; 125:483–495.
Agger K, Cloos PA, Christensen J, et al. UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature 2007; 449:731–734.
Stern CD . Neural induction: old problem, new findings, yet more questions. Development 2005; 132:2007–2021.
Wilson SI, Graziano E, Harland R, Jessell TM, Edlund T . An early requirement for FGF signalling in the acquisition of neural cell fate in the chick embryo. Curr Biol 2000; 10:421–429.
Kunath T, Saba-El-Leil MK, Almousailleakh M, et al. FGF stimulation of the Erk1/2 signalling cascade triggers transition of pluripotent embryonic stem cells from self-renewal to lineage commitment. Development 2007; 134:2895–2902.
Tropepe V, Hitoshi S, Sirard C, et al. Direct neural fate specification from embryonic stem cells: a primitive mammalian neural stem cell stage acquired through a default mechanism. Neuron 2001; 30:65–78.
Stavridis MP, Lunn JS, Collins BJ, Storey KG . A discrete period of FGF-induced Erk1/2 signalling is required for vertebrate neural specification. Development 2007; 134:2889–2894.
LaVaute TM, Yoo YD, Pankratz MT, et al. Regulation of neural specification from human embryonic stem cells by BMP and FGF. Stem Cells 2009; 27:1741–1749.
Finley MF, Devata S, Huettner JE . BMP-4 inhibits neural differentiation of murine embryonic stem cells. J Neurobiol 1999; 40:271–287.
Kawasaki H, Mizuseki K, Nishikawa S, et al. Induction of midbrain dopaminergic neurons from ES cells by stromal cell-derived inducing activity. Neuron 2000; 28:31–40.
Allis CD, Berger SL, Cote J, et al. New nomenclature for chromatin-modifying enzymes. Cell 2007; 131:633–636.
Chen Z, Zang J, Kappler J, et al. Structural basis of the recognition of a methylated histone tail by JMJD2A. Proc Natl Acad Sci USA 2007; 104:10818–10823.
Chen Z, Zang J, Whetstine J, et al. Structural insights into histone demethylation by JMJD2 family members. Cell 2006; 125:691–702.
Couture JF, Collazo E, Ortiz-Tello PA, Brunzelle JS, Trievel RC . Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase. Nat Struct Mol Biol 2007; 14:689–695.
Ng SS, Kavanagh KL, McDonough MA, et al. Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity. Nature 2007; 448:87–91.
Frescas D, Guardavaccaro D, Bassermann F, Koyama-Nasu R, Pagano M . JHDM1B/FBXL10 is a nucleolar protein that represses transcription of ribosomal RNA genes. Nature 2007; 450:309–313.
He J, Kallin EM, Tsukada Y, Zhang Y . The H3K36 demethylase Jhdm1b/Kdm2b regulates cell proliferation and senescence through p15(Ink4b). Nat Struct Mol Biol 2008; 15:1169–1175.
Agger K, Christensen J, Cloos PA, Helin K . The emerging functions of histone demethylases. Curr Opin Genet Dev 2008; 18:159–168.
Shi Y . Histone lysine demethylases: emerging roles in development, physiology and disease. Nat Rev Genet 2007; 8:829–833.
Wang J, Hevi S, Kurash JK, et al. The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation. Nat Genet 2009; 41:125–129.
Wang J, Scully K, Zhu X, et al. Opposing LSD1 complexes function in developmental gene activation and repression programmes. Nature 2007; 446:882–887.
Shi X, Hong T, Walter KL, et al. ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature 2006; 442:96–99.
Wysocka J, Swigut T, Xiao H, et al. A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling. Nature 2006; 442:86–90.
Watanabe K, Kamiya D, Nishiyama A, et al. Directed differentiation of telencephalic precursors from embryonic stem cells. Nat Neurosci 2005; 8:288–296.
Acknowledgements
We thank Anning Lin (The University of Chicago) for the critical reading of the paper, members in the Chen lab for technical help, the cell biology and molecular biology core facilities for confocal study and Q-PCR, and Shanghai Biochip Co Ltd. for microarray analysis. The H3K27me2 antibody was kindly provided by Li Tang (Fudan University) and Thomas Jenuwein (Research Institute of Molecular Pathology, The Vienna Biocenter). This work was supported by the National Basic Research Program of China (2007CB957900, 2006CB943902, 2007CB947101, 2008KR0695, 2009CB941100, 2005CB522704), the Chinese Academy of Sciences (KSCX2-YW-R-04), the National Natural Science Foundation of China (90919026, 30870538,30623003, 30721065, 30830034, 90919046), the Shanghai Pujiang Program (0757S11361), the Shanghai Key Project of Basic Science Research (06DJ14001, 06DZ22032, 08DJ1400501), and the Council of Shanghai Municipal Government for Science and Technology (088014199).
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The original online version of this article was revised: Figure 4 was corrected.
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Supplementary information, Figure S1 (download PDF )
Gene Ontology (GO) hierarchy for enriched biological process categories. (PDF 206 kb)
Supplementary information, Figure S2 (download PDF )
Knockdown of KIAA1718 blocked neural differentiation. (PDF 144 kb)
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Huang, C., Xiang, Y., Wang, Y. et al. Dual-specificity histone demethylase KIAA1718 (KDM7A) regulates neural differentiation through FGF4. Cell Res 20, 154–165 (2010). https://doi.org/10.1038/cr.2010.5
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DOI: https://doi.org/10.1038/cr.2010.5
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